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At least 19 recordsLinked to original sources
USGS2015

Experimental infection of snakes with Ophidiomyces ophiodiicola causes pathological changes that typify snake fungal disease

Snake fungal disease (SFD) is an emerging skin infection of wild snakes in eastern North America. The fungus Ophidiomyces ophiodiicola is frequently associated with the skin lesions that are characteristic of SFD, but a causal relationship between the fungus and the disease has not been established. We experimentally infected captive-bred corn snakes ( Pantherophis guttatus ) in the laboratory with pure cultures of O. ophiodiicola . All snakes in the infected group ( n = 8) developed gross and microscopic lesions identical to those observed in wild snakes with SFD; snakes in the control group ( n = 7) did not develop skin infections. Furthermore, the same strain of O. ophiodiicola used to inoculate snakes was recovered from lesions of all animals in the infected group, but no fungi were isolated from individuals in the control group. Monitoring progression of lesions throughout the experiment captured a range of presentations of SFD that have been described in wild snakes. The host response to the infection included marked recruitment of granulocytes to sites of fungal invasion, increased frequency of molting, and abnormal behaviors, such as anorexia and resting in conspicuous areas of enclosures. While these responses may help snakes to fight infection, they could also impact host fitness and may contribute to mortality in wild snakes with chronic O. ophiodiicola infection. This work provides a basis for understanding the pathogenicity of O. ophiodiicola and the ecology of SFD by using a model system that incorporates a host species that is easy to procure and maintain in the laboratory. IMPORTANCE Skin infections in snakes, referred to as snake fungal disease (SFD), have been reported with increasing frequency in wild snakes in the eastern United States. While most of these infections are associated with the fungus Ophidiomyces ophiodiicola , there has been no conclusive evidence to implicate this fungus as a primary pathogen. Furthermore, it is not understood why the infections affect different host populations differently. Our experiment demonstrates that O. ophiodiicola is the causative agent of SFD and can elicit pathological changes that likely impact fitness of wild snakes. This information, and the laboratory model we describe, will be essential in addressing unresolved questions regarding disease ecology and outcomes of O. ophiodiicola infection and helping to conserve snake populations threatened by the disease. The SFD model of infection also offers utility for exploring larger concepts related to comparative fungal virulence, host response, and host-pathogen evolution.

mBio↗
USGS2004

Water Quality of the Snake River and Five Eastern Tributaries in the Upper Snake River Basin, Grand Teton National Park, Wyoming, 1998-2002

To address water-resource management objectives of the National Park Service in Grand Teton National Park, the U.S. Geological Survey in cooperation with the National Park Service has conducted water-quality sampling in the upper Snake River Basin. Routine sampling of the Snake River was conducted during water years 1998-2002 to monitor the water quality of the Snake River through time. A synoptic study during 2002 was conducted to supplement the routine Snake River sampling and establish baseline water-quality conditions of five of its eastern tributaries?Pilgrim Creek, Pacific Creek, Buffalo Fork, Spread Creek, and Ditch Creek. Samples from the Snake River and the five tributaries were collected at 12 sites and analyzed for field measurements, major ions and dissolved solids, nutrients, selected trace metals, pesticides, and suspended sediment. In addition, the eastern tributaries were sampled for fecal-indicator bacteria by the National Park Service during the synoptic study. Major-ion chemistry of the Snake River varies between an upstream site above Jackson Lake near the northern boundary of Grand Teton National Park and a downstream site near the southern boundary of the Park, in part owing to the inputs from the eastern tributaries. Water type of the Snake River changes from sodium bicarbonate at the upstream site to calcium bicarbonate at the downstream site. The water type of the five eastern tributaries is calcium bicarbonate. Dissolved solids in samples collected from the Snake River were significantly higher at the upstream site (p-value<0.001), where concentrations in 43 samples ranged from 62 to 240 milligrams per liter, compared to the downstream site where concentrations in 33 samples ranged from 77 to 141 milligrams per liter. Major-ion chemistry of Pilgrim Creek, Pacific Creek, Buffalo Fork, Spread Creek, and Ditch Creek generally did not change substantially between the upstream sites near the National Park Service boundary with the National Forest and the downstream sites near the Snake River; however, variations in the major ions and dissolved solids existed between basins. Variations probably result from differences in geology between the tributary basins. Concentrations of dissolved ammonia, nitrite, and nitrate in all samples collected from the Snake River and the five eastern tributaries were less than water-quality criteria for surface waters in Wyoming. Concentrations of total nitrogen and total phosphorus in samples from the Snake River and the tributaries generally were less than median concentrations determined for undeveloped streams in the United States; however, concentrations in some samples did exceed ambient total-nitrogen and total-phosphorus criteria for forested mountain streams in the Middle Rockies ecoregion recommended by the U.S. Environmental Protection Agency to address cultural eutrophication. Sources for the excess nitrogen and phosphorus probably are natural because these basins have little development and cultivation. Concentrations of trace metals and pesticides were low and less than water-quality criteria for surface waters in Wyoming in samples collected from the Snake River and the five eastern tributaries. Atrazine, dieldrin, EPTC, or tebuthiuron were detected in estimated concentrations of 0.003 microgram per liter or less in 5 of 27 samples collected from the Snake River. An estimated concentration of 0.008 microgram per liter of metolachlor was detected in one sample from the Buffalo Fork. The estimated concentrations were less than the reporting levels for the pesticide analytical method. Suspended-sediment concentrations in 43 samples from the upstream site on the Snake River ranged from 1 to 604 milligrams per liter and were similar to suspended-sediment concentrations in 33 samples from the downstream site, which ranged from 1 to 648 milligrams per liter. Suspended-sediment concentrations in 38 samples collected from the tributary streams ranged from 1 t

Scientific Investigations Report↗
USGS2023

Prevalence of Ophidiomyces ophidiicola and epizootiology of snake fungal disease in free-ranging Northern Pine Snakes (Pituophis melanoleucus melanoleucus) in New Jersey

Snake fungal disease, caused by Ophidiomyces ophidiicola , is recognized as a potential concern for North American snakes. We tested skin swabs from Northern Pine Snakes ( Pituophis melanoleucus melanoleucus ) in the New Jersey pinelands for the presence of O. ophidiicola before emergence from hibernation. We used qPCR to test the collected swabs for the presence of O. ophidiicola , then determined pathogen prevalence as a function of sampling year, sampling location (skin lesion, healthy ventral skin, healthy head skin) sex, and age . There were no temporal trends in O. ophidiicola detection percentages on snakes, which varied from 58 to 83% in different years. Ophidiomyces ophidiicola detection on snakes was highest in swabs of skin lesions (71%) and lowest in head swabs (29%). Males had higher prevalence than females (82% versus 62%). The fungus was not detected in hatchling snakes (age 0) in the fall, but 75% of juveniles tested positive at the end of hibernation (age 1 year). We also screened hibernacula soil samples for the presence of O. ophidiicola . Where snakes hibernated, 69% of soil samples were positive for O. ophidiicola , and 85% of snakes lying on positive soil samples also tested positive for the pathogen. Although a high proportion of snakes (73%) tested positive for O. ophidiicola during our 4-year study , the snakes appeared healthy except for small skin lesions. We conclude that O. ophidiicola prevalence is high on hibernating Northern Pine Snakes and in the hibernacula soil, with a strong association between snakes and positive adjacent soil. This is the first demonstration that snakes likely become infected during hibernation.

New Jersey↗
USGS1971

History of Snake River Canyon indicated by revised stratigraphy of Snake River Group near Hagerman and King Hill, Idaho

A discovery that debris left by the Bonneville Flood (Melon Gravel) overlies McKinney Basalt about 200 feet above the Snake River near King Hill requires that the stratigraphy of the Snake River Group be revised. In former usage, the McKinney Basalt and its immediately older companion, the Wendell Grade Basalt, were considered on the basis of equivocal field relations to be younger than the Melon Gravel and were assigned to the Recent. These lava flows are here reclassified as Pleistocene. The Bancroft Springs Basalt, which consists of both subaerial lava and pillow lava in a former Snake River canyon, was previously separated from the McKinney but is now combined with the McKinney. Accordingly, the name Bancroft Springs Basalt is here abandoned. This revised stratigraphy is first described from geomorphic relations of the McKinney Basalt near King Hill and is then discussed in the light of drainage changes caused by local lava flows during entrenchment of the Snake River. Near King Hill, a former Snake River canyon was completely filled by McKinney Basalt at the place called Bancroft Springs, hut the depth of this lava in the next several miles of the canyon downstream (along a route that approximately coincides with the present canyon) steadily decreased. This ancestral geomorphology is inferred from the former canyon route and, also, from the continuity in gradient of the McKinney lava surface downstream from Bancroft Springs. The drainage history recorded by various lava flows and river deposits of the Snake River Group indicates that the McKinney and Wendell Grade Basalts erupted after the Snake River canyon had reached its present depth of about 500 feet. The Snake River of that time, as far downstream as Bliss, flowed approximately along its present route. The Wood River of that time, however, skirted the north flank of Gooding Butte and joined the ancestral Snake at a junction, now concealed by lava, north of the present canyon about 3 miles west of Bliss. From that place the former Snake River canyon, also now concealed by lava, continued west to Bancroft Springs and thence along a route close to the present canyon to King Hill. To become entrenched in a canyon 500 feet deep, the Snake River downstream from Hagerman became progressively more incised while its upstream route was pushed south in several earlier canyons by intermittent lava flows. Distinctive gravel deposits help to establish the episodes of progressive canyon cutting and to determine the routes of ancestral drainage, including the former position of the Wood River. As canyon cutting continued, springs began to emerge where lavas had filled the earlier canyons. When the Snake River canyon eventually attained its approximate present depth, the Wendell Grade Basalt erupted near Shoshone and, as several tongues, spread west to the canyon rim opposite Hagerman. One tongue crossed the future route of the Wood River, and another covered an upland area of Sand Springs Basalt that had previously reached the canyon floor at Hagerman. The McKinney Basalt then erupted from McKinney Butte northeast of Bliss and spread southward as a subaerial flow, covering part of the Wendell Grade Basalt. It filled the ancestral Wood River canyon and the Snake River canyon of that time west of Bliss as far downstream as King Hill. The resulting dam of lava impounded a deep lake, which extended upstream in the canyon beyond Hagerman. Copious amounts of the McKinney spilled into this temporary lake and produced pillow lava. About 2 miles west of Bliss, pillow lava 500 feet thick completely fills the former canyon and is protected by rimrock of the subaerial McKinney Basalt. From Bliss, the pillow facies extends upstream as far as the McKinney rimrock - about 5 miles. Eruption of the McKinney Basalt diverted the Wood River to a course along the southeast edge of this lava flow. The temporary lake that was dammed by McKinney Basalt west of Bliss spilled along the sou

Idaho↗
USGS1991

Effect of experience with pine (Pituophis melanoleucus) and king (Lampropeltis getulus) snake odors on Y-maze behavior of pine snake hatchlings

The abilities of hatchling pine snakes ( Pituophis melanoleucus ) and king snakes ( Lampropeltis getulus ) to discriminate the chemical trails of pine and king snakes was investigated in Y -maze experiments. Pine snakes were housed for 17 days either with shavings impregnated with pine snake odor, king snake odor, or no odor to test for the effect of experience on choice. Both pine and king snake hatchlings entered the arm with the pine snake odor and did not enter the arm with the king snake odor. The data support the hypothesis that hatchlings of both species can distinguish conspecific odors from other odors and that our manipulation of previous experience was without effect for pine snake hatchlings.

Journal of Chemical Ecology↗
USGS1992

Streamflow gains and losses in the Snake River and ground-water budgets for the Snake River Plain, Idaho and eastern Oregon

The Snake River is the regional drain for streams and aquifers in the Snake River basin upstream from Weiser, Idaho. The interaction between the river and ground water was quantified as streamflow gains from and losses to the aquifers. Upstream from Milner, Idaho, the Snake River both gains and loses water. Some reaches gain or lose throughout the year; other reaches gain during the irrigation season when ground-water levels rise as a result of application of surface water for irrigation but lose during the rest of the year. The largest continuous streamflow gain upstream from Milner is from springs between Blackfoot and Neeley, where, in 1980, the Snake River gained 1.9 million acre-feet of ground water. Downstream from Milner, the Snake River is a gaining stream. Gains arc largest between Milner and King Hill where numerous springs discharge to the river. In 1980, the Snake River gained 4.7 million acre-feet of ground water between Milner and King Hill. Although large springs were present in the Blackfoot-to-Neeley and Milner-to-King Hill reaches before irrigation began on the plain, the application of surface water for irrigation increased recharge to the Snake River Plain aquifer; therefore, spring discharge to both reaches also increased. However, despite changes in irrigated acreage and corresponding changes in the amount of water potentially available for recharge, spring discharge between Blackfoot and Neeley has remained relatively stable for 69 years (1912-80). During the same period, discharge from individual springs and total ground-water discharge between Milner and King Hill have increased and decreased substantially in quantities that can be attributed to changes in irrigation. The changes in ground-water recharge and discharge and ground-water storage generally are the net result of 100 successive years of irrigation on the Snake River Plain. Water-budget analyses indicate that the total volume of ground water in storage in the main part of the eastern Snake River Plain increased about 24 million acre-feet from 1880 to 1952, largely as a result of increased recharge in areas irrigated with surface water. The total volume of ground water in storage decreased about 6 million acre-feet from 1952 to 1980 as a result of several years of below-normal precipitation, increased pumping of ground water for irrigation, and other changes in irrigation practices. Ground-water storage in parts of the western plain increased about 3 million acre-feet from 1930 to 1972 but generally has decreased since 1972.

Idaho, Oregon↗
USGS2021

Effects of snake fungal disease on short‐term survival, behavior, and movement in free‐ranging snakes

Pathogenic fungi are increasingly associated with epidemics in wildlife populations. Snake fungal disease (SFD, also referred to as Ophidiomycosis) is an emerging threat to snakes, taxa that are elusive and difficult to sample. Thus, assessments of the effects of SFD on populations have rarely occurred. We used a field technique to enhance detection, Passive Integrated Transponder (PIT) telemetry, and a multi‐state capture–mark–recapture model to assess SFD effects on short‐term (within‐season) survival, movement, and surface activity of two wild snake species, Regina septemvittata (Queensnake) and Nerodia sipedon (Common Watersnake). We were unable to detect an effect of disease state on short‐term survival for either species. However, we estimated Bayesian posterior probabilities of >0.99 that R. septemvittata with SFD spent more time surface‐active and were less likely to permanently emigrate from the study area. We also estimated probabilities of 0.98 and 0.87 that temporary immigration and temporary emigration rates, respectively, were lower in diseased R. septemvittata . We found evidence of elevated surface activity and lower temporary immigration rates in diseased N. sipedon , with estimated probabilities of 0.89, and found considerably less support for differences in permanent or temporary emigration rates. This study is the first to yield estimates for key demographic and behavioral parameters (survival, emigration, surface activity) of snakes in wild populations afflicted with SFD. Given the increase in surface activity of diseased snakes, future surveys of snake populations could benefit from exploring longer‐term demographic consequences of SFD and recognize that disease prevalence in surface‐active animals may exceed that of the population as a whole.

Ecological Applications↗
USGS2025

Mortality event in rainbow snakes linked to snake fungal disease, United States

We report mortality in rainbow snakes in Virginia and North Carolina, USA, linked to snake fungal disease caused by Ophidiomyces ophidiicola . During 2013–2023, we observed 46 dead rainbow snakes with lesions indicative of snake fungal disease, noted elevated disease severity compared with other species, and recorded fewer live snakes over time.

North Carolina, Virginia↗
USGS2007

Molecular and phenotypic diversity in Chionactis occipitalis (Western Shovel-nosed Snake), with emphasis on the status of C. o. klauberi (Tucson Shovel-nosed Snake).

Chionactis occipitalis (Western Shovel-nosed Snake) is a small colubrid snake inhabiting the arid regions of the Mojave, Sonoran, and Colorado deserts. Morphological assessments of taxonomy currently recognize four subspecies. However, these taxonomic proposals were largely based on weak morphological differentiation and inadequate geographic sampling. Our goal was to explore evolutionary relationships and boundaries among subspecies of C. occipitalis, with particular focus on individuals within the known range of C. o. klauberi (Tucson Shovel-nosed snake). Population sizes and range for C. o. klauberi have declined over the last 25 years due to habitat alteration and loss prompting a petition to list this subspecies as endangered. We examined the phylogeography, population structure, and subspecific taxonomy of C. occipitalis across its geographic range with genetic analysis of 1100 bases of mitochondrial DNA sequence and reanalysis of 14 morphological characters from 1543 museum specimens. We estimated the species gene phylogeny from 81 snakes using Bayesian inference and explored possible factors influencing genetic variation using landscape genetic analyses. Phylogenetic and population genetic analyses reveal genetic isolation and independent evolutionary trajectories for two primary clades. Our data indicate that diversification between these clades has developed as a result of both historical vicariance and environmental isolating mechanisms. Thus these two clades likely comprise 'evolutionary significant units' (ESUs). Neither molecular nor morphological data are concordant with the traditional C. occipitalis subspecies taxonomy. Mitochondrial sequences suggest specimens recognized as C. o. klauberi are embedded in a larger geographic clade whose range has expanded from western Arizona populations, and these data are concordant with clinal longitudinal variation in morphology. ?? 2007 Springer Science+Business Media B.V.

Conservation Genetics↗
USGS2016

Snake fungal disease: An emerging threat to wild snakes

Since 2006, there has been a marked increase in the number of reports of severe and often fatal fungal skin infections in wild snakes in the eastern USA. The emerging condition, referred to as snake fungal disease (SFD), was initially documented in rattlesnakes, where the infections were believed to pose a risk to the viability of affected populations. The disease is caused by Ophidiomyces ophiodiicola , a fungus recently split from a complex of fungi long referred to as the Chrysosporium anamorph of Nannizziopsis vriesii (CANV). Here we review the current state of knowledge about O. ophiodiicola and SFD. In addition, we provide original findings which demonstrate that O. ophiodiicola is widely distributed in eastern North America, has a broad host range, is the predominant cause of fungal skin infections in wild snakes and often causes mild infections in snakes emerging from hibernation. This new information, together with what is already available in the scientific literature, advances our knowledge of the cause, pathogenesis and ecology of SFD. However, additional research is necessary to elucidate the factors driving the emergence of this disease and develop strategies to mitigate its impacts.

Philosophical Transactions of the Royal Society B:↗
USGS2016

First documented case of snake fungal disease in a free-ranging wild snake in Louisiana

Snake fungal disease (SFD) is a recently documented mycotic disease characterized by scabs or crusty scales, subcutaneous nodules, abnormal molting, cloudiness of the eyes (not associated with molting), and localized thickening or crusting of the skin. SFD has been documented in many species in the Eastern and Midwestern United States within the last decade. SFD has proven lethal in many snakes, and the disease is recognized as an emerging threat to wild snake populations. Here, we describe the first documented case of SFD in Louisiana in a free-ranging wild snake.

Louisiana↗
USGS2012

The Yellowstone-Snake River Plain seismic profiling experiment: Crustal structure of the Eastern Snake River Plain

Seismic refraction profiles recorded along the eastern Snake River Plain (ESRP) in southeastern Idaho during the 1978 Yellowstone-Snake River Plain cooperative seismic profiling experiment are interpreted to infer the crustal velocity and attenuation (Q-1) structure of the ESRP. Travel-time and synthetic seismogram modeling of a 250 km reversed refraction profile as well as a 100 km detailed profile indicate that the crust of the ESRP is highly anomalous. Approximately 3 to 6 km of volcanic rocks (with some interbedded sediments) overlie an upper-crustal layer (compressional velocity ≅6.1 km/s) which thins southwestward along the ESRP from a thickness of 10 km near Island Park Caldera to 2 to 3 km beneath the central and southwestern portions of the ESRP. An intermediate-velocity (≅6.5 km/s) layer extends from ≅10 to ≅20 km depth. A thick (≅22 km) lower crust of compressional velocity 6.8 km/s, a total crustal thickness of ≅42 km, and a P n velocity of ≅7.9 km/s is observed in the ESRP, similar to the western Snake River Plain and the Rocky Mountains Provinces. High attenuation is evident on the amplitude corrected seismic data due to low-Q values in the volcanic rocks (Q p = 20 to 200) and throughout the crust (Q p = 160 to 300). Based on these characteristics of the crustal structure and volcanic-age progression data, it is suggested that the ESRP has resulted from an intensive period of intrusion of mantle-derived basaltic magma into the upper crust generating explosive silicic volcanism and associated regional uplift and caldera collapse. This activity began about 15 m.y. ago in southwestern Idaho and has migrated northeast to its present position at Yellowstone. Subsequent cooling of the intruded upper crust results in the 6.5 km/s velocity intermediate layer. Crustal subsidence and periodic basaltic volcanism as represented by the ESRP complete the sequence of crustal evolution.

Journal of Geophysical Research B: Solid Earth↗
USGS1984

Flow characteristics of the Snake River and water budget for the Snake River plain, Idaho and eastern Oregon

This report is one in a series resulting from the U.S. Geological Survey's Snake River Plain Rasa (Regional Aquifer System Analysis) study that was initiation in October 1979. Purposes of the RASA study were to (1) refine knowledge of the regional ground-water flow system, (2) determine effects of conjunctive use of ground water and surface water, and (3) describe water chemistry. This purpose of this report is to describe flow characteristics of the Snake River and tributaries and to develop a water budget for the Snake River Plain. Data and interpretation in this report will be used in development of ground-water flow models.

Idaho, Oregon↗
USGS2012

Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus ), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus , and Clark's Nutcracker, Nucifraga columbiana ), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample &ndash; a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.

PLoS ONE↗
USGS1995

Streamflow gains and losses in the Snake River and ground-water budgets for the Snake River plain, Idaho and eastern Oregon

Streamflow gains and losses in the Snake River demonstrate ground-water and surface-water relations and are used to develop ground-water budgets for the Snake River plain. Budgets indicate the storage in the eastern plain increased by 24 million acre-feet from 1880 to 1952 and, in the western plain, increased by about 3 million acre-feet from 1930 to 1972. Ground-water storage throughout the plain has declined in recent years, owing to climatic variations and changing irrigation practices.

Professional Paper↗